GSEA with mouse RNAseq data
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3.4 years ago
Alex Gibbs ▴ 80

Hi everyone,

I have had RNAseq performed on mouse samples (12 samples, 4 groups) and have the results ready to plug into Gene Set Enrichment Analysis (GSEA) software.

I notice that there are plenty of human gene sets available on MSigDB, but not many for mouse. I would like to run GSEA with 6 signalling pathway gene sets, but the only ones I can find are for human. Does anyone know if the human signalling pathways are exactly the same as mouse signalling pathways? Or is there a mouse database that I can go onto to download mouse specific signalling pathway gene sets?

Thank you in advance!

Alex

RNA-Seq • 4.6k views
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MSigDB pathways are presented as human symbols, but are based on multiple species.

Related discussion: GSEA analysis with Mouse (Please give some comments..)

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2.1 years ago
Gordon Smyth ★ 4.8k

We created a mouse version of the MSigDB, available from http://bioinf.wehi.edu.au/MSigDB/

Our version is designed for use with R so the gene sets are provided as native R objects.

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Why don't you provide them in ".gmt" format for direct download/load on GSEA?

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It works just as well as they are. You can easily output the data objects in GMT format, if you wish.

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3.4 years ago
Buffo ★ 1.9k

You can use webgestalt, it has a list of organisms (including mouse)

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15 months ago

Another answer: you can retrieve these gene sets automatically via msigdbr, too: https://cran.r-project.org/web/packages/msigdbr/vignettes/msigdbr-intro.html

Kevin

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